Bacteria persisting in a biofilm in the mammalian body cause about two-thirds of all chronic/recurrent diseases. These biofilms are comprised of bacteria protected by an outer “slime” that is often comprised primarily of DNA that prevents the innate and adaptive immune systems, antibiotics and other antibacterial agents from gaining access to the bacteria inside the biofilm, making it extremely difficult to clear the infection from the body. Furthermore, the biofilm can act as a reservoir for future acute infections often with lethal consequences.
At least one protein from the DNABII family of proteins are found in all known eubacteria and are naturally found outside of the bacterial cell. While they elicit a strong innate immune response, host subjects fail to naturally produce specific antibody to family members as a result of infection. The major problem with bacterial biofilms is the inability of the host immune system and/or antibiotics and other antimicrobials to gain access to the bacteria protected within the biofilm.
Biofilms are present in an industrial setting as well. For example, biofilms are implicated in a wide range of petroleum process problems, from the production field to the gas station storage tank. In the field, sulfate reducing biofilm bacteria produce hydrogen sulfide (soured oil). In the process pipelines, biofilm activity develops slimes which impede filters and orifices. Biofilm and biofilm organisms also cause corrosion of pipeline and petroleum process equipment. These problems can be manifested throughout an oil or gas production facility to the point where fouling and corrosive biofilm organisms have even been found on the surfaces of final product storage tanks.
In the home, biofilms are found in or on any surface that supports microbial growth, e.g., in drains, on food preparation surfaces, in toilets, and in swimming pools and spas.
Biofilms are implicated in a wide range of water processes, both domestic and industrial. They can grow on the surface of process equipment and impede the performance of the equipment, such as degradation of heat transfer or plugging of filters and membranes. Biofilms growing on a cooling tower fill can add enough weight to cause collapse of the fill. Biofilms cause corrosion of even highly specialized stainless steels. Biofilms in a water process can degrade the value of a final product such as biofilm contamination in a paper process or the attachment of even a single cell on a silicon chip. Biofilms growing in drinking water distribution systems can harbor potential pathogenic organisms, corrosive organisms or bacteria that degrade the aesthetic quality of the water.
Thus, a need exists to break through the protective barrier of biofilms to treat or kill the associated bacterial infections and clear them from surfaces and in water systems. This invention satisfies this need and provides related advantages as well.
SEQUENCE LISTINGSEQ. ID NO. 1A1-A2-A3-A4-A5-A6-A7-A8-A9wherein:A1 is V or I;A2 is any one of K, Q, E, A, V or Y;A3 is any one of K, L, I, V or F;A4 is any one of S, I, R or V;A5 is any one of G or S;A6 is F;A7 is G;A8 is any one of N or S or T or K; andA9 is F. SEQ. ID NO. 2 is VKKSGFGNF SEQ ID NO. 3 is B1-B2-B3-B4-B5-B5-B6-B7wherein:B1 is absent or any one of G or K;B2 is absent or any one of R, I or K;B3 is N or V;B4 is P or I;B5 is any one of K, Q, S or G;B6 is any one of T, K or S; andB7 is any one of U, K, Q or D. Seq. ID NO. 4 is NP(K/Q)TG Seq. ID NO. 5 GRNP(K/Q)TG Seq. ID NO. 6 Full Length Wild type (wt) 86-028NP Haemophilus influenzae IhfA;Genbank accession No.: AAX88425.1, last accessed Mar. 21, 2011:MATITKLDIIEYLSDKYHLSKQDTKNVVENFLEEIRLSLESGQDVKLSGFGNFELRDKSSRPGRNPKTGDVVPVSARRVVITKPGQKLRARVEKIK Seq. ID NO. 7 Full Length wt 86-028NP Haemophilus influenzae HU, Genbank accessionNo.: YP_248142.1, last accessed Mar. 21, 2011: MRFVTIFINHAFNSSQVRLSFAQFLRQIRKDTFKESNFLFNRRYKFMNKTDLIDAIANAAELNKKQAKAALEATLDAITASLKEGEPVQLIGFGTFKVNERAARTGRNPQTGAEIQIAASKVPAFVSGKALKDAIK Seq. ID NO. 8 Full Length wt R2846 Haemophilus influenzae MA, Genbank accessionNo.: ADO96375, last accessed Mar. 21, 2011:MATITKLDIIEYLSDKYHLSKQDTKNVVENFLEEIRLSLESGQDVKLSGFGNFELRDKSSRPGRNPKTGDVVPVSARRVVTFKPGQKLRARVEKTK Seq. ID NO. 9 Full Length wt Rd Haemophilus influenzae IhfA; Genbank accession No.:AAC22959.1, last accessed Mar. 21, 2011: MATITKLDIIEYLSDKYHLSKQDTKNVVENFLEEIRLSLESGQDVKLSGFGNFELRDKSSRPGRNPKTGDVVPVSARRVVTFKPGQKLRARVEKTK; Seq. ID NO. 10 Full Length wt E. coli K12 IhfA; Genbank accession No.: AAC74782.1,last accessed Mar. 21, 2011: MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE,; DNA Genbank No. NC_000913 Seq. ID NO. 11 Full Length wt P. aeruginosa PA 01 IhfA; Genbank accession No.:AAG06126.1, last accessed Mar. 21, 2011: MGALTKAEIAERLYEELGLNKREAKELVELFFEEIRQALEHNEQVKLSGFGNFDLRDKRQRPGRNPKTGEEIPITARRVVTFRPGQKLKARVEAYAGTKS Seq ID NOS. 12 and 13: β-3 and α-3 portions of (IHFα) SEQ ID NO. 12: TFRPGQ andSEQ ID NO. 13: KLKSRVENASPKDE Seq ID NOS. 14 and 15: β-3 and α-3 portions of (IHFα) SEQ ID NO. 14: HFKPGK andSEQ ID NO 15: ELRDRANIYG Seq ID NOS. 16 and 17: β-3 and α-3 portions of SEQ ID NOS. 6, SEQ. ID NOS. 16:TFKPGQ and SEQ ID NO. 17: KLRARVEKTK SEQ ID NOS. 18 and 19: β-3 and α-3 portions of 2019 Haemophilus influenzae IhfA,SEQ ID NO. 18: TFKPGQ and SEQ ID NO. 19: KLRARVENTK SEQ ID NOS. 20 and 21: β-3 and α-3 portions of SEQ. ID NO. 8, SEQ ID NO. 20:TFKPGQ and SEQ ID NO. 21: KLRARVEKTK SEQ ID NOS. 22 and 23: β-3 and α-3 portions of SEQ ID NO. 9, SEQ ID NO. 22:TFKPGQ and SEQ ID NO. 23: KLRARVEKTK SEQ ID NOS. 24 and 25: β-3 and α-3 portions of SEQ ID NO. 10, SEQ ID NO. 24:TFRPGQ and SEQ ID NO. 25: KLKSRVENASPKDE SEQ ID NOS. 26 and 27: β-3 and α-3 portions of SEQ ID NO. 11, SEQ ID NO. 26:TFRPGQ and SEQ ID NO, 27: KLKARVEAYAGTKS SEQ ID NO. 28: E. coli hupA, Genbank accession No.: AP_003818,Last accessed Mar. 21, 2011: MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK SEQ ID NO. 29: E. coli hupB, Genbank accession No.: AP_001090.1,Last accessed Mar. 21, 2011: MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEIAAAKVPSFRAGKALKDAVN SEQ ID NOS. 30 and 31: β-3 and α-3 portions of SEQ ID NO. 28, SEQ ID NO. 30:AFVSGK and SEQ ID NO. 31: ALKDAVK SEQ ID NOS. 32 and 33: β-3 and α-3 portions of SEQ ID NO. 29, SEQ ID NO. 32:STRAGK and SEQ ID NO. 33: ALKDAVN SEQ. ID NO. 34: C-terminal 20 amino acids of IHF α: TFRPGQKLKSRVENASPKDE SEQ. ID NO. 35: C-terminal 20 amino acids of IHF β: KYVPHFKPGKELRDRANIYG SEQ. ID NO. 36: DNABII binding consensus sequence: WATCAANNNNTTR wherein Wis A or T, N is any base and R is a purine SEQ. ID NO. 337: E. coli IHFalpha: GRNPKTGEDIPI SEQ. ID NO. 338: E. coli IHFbeta: GRNPKTGDKVEL SEQ. ID NO. 339: E. coli HUalpha: GRNPQTGKEIKI SEQ. ID NO. 340: E. coli HUbeta: GRNPQTGKEITI